5ZNJ

Crystal structure of a bacterial ProRS with ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.

Cheng, B.Cai, Z.Luo, Z.Luo, S.Luo, Z.Cheng, Y.Yu, Y.Guo, J.Ju, Y.Gu, Q.Xu, J.Jiang, X.Li, G.Zhou, H.

(2022) J Med Chem 65: 15840-15855

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01496
  • Primary Citation of Related Structures:  
    5ZNJ, 5ZNK

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (aaRSs) are promising antimicrobial targets due to their essential roles in protein translation, and expanding their inhibitory mechanisms will provide new opportunities for drug discovery. We report here that halofuginone (HF), an herb-derived medicine, moderately inhibits prolyl-tRNA synthetases (ProRSs) from various pathogenic bacteria. A cocrystal structure of Staphylococcus aureus ProRS ( Sa ProRS) with HF and an ATP analog was determined, which guided the design of new HF analogs. Compound 3 potently inhibited Sa ProRS at IC 50 = 0.18 μM and K d = 30.3 nM and showed antibacterial activities with an MIC of 1-4 μg/mL in vitro . The bacterial drug resistance to 3 only developed at a rate similar to or slower than those of clinically used antibiotics in vitro . Our study indicates that the scaffold and ATP-aided inhibitory mechanism of HF could apply to bacterial ProRS and also provides a chemical validation for using bacterial ProRS as an antibacterial target.


  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline--tRNA ligase567Staphylococcus aureusMutation(s): 0 
Gene Names: proSCT123_02285
EC: 6.1.1.15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
HFG
Query on HFG

Download Ideal Coordinates CCD File 
C [auth A]7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one
C16 H17 Br Cl N3 O3
LVASCWIMLIKXLA-CABCVRRESA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.139α = 90
b = 77.535β = 99.36
c = 74.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81773636

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description